champ.DMR() error ..... "cannot allocate vector of size 56.5 Mb"

[ronfinn]

Hi Tian,

I am getting the follwoing error when I rerun the ChAMP pipeline with the test data provided:

Running champ.DMR()...
[===========================]
[<<<<< ChAMP.DMR START >>>>>]
-----------------------------
!!! important !!! We just upgrate champ.DMR() function, since now champ.DMP() could works on multiple phenotypes, but ProbeLasso can only works on one DMP result, so if your pheno parameter contains more than 2 phenotypes, and you want to use ProbeLasso function, you MUST specify compare.group=c("A","B"). Bumphunter and DMRcate should not be influenced.

[ Section 1:  Check Input Pheno Start ]

  You pheno is character type.
    Your pheno information contains following groups. >>
    <C>:4 samples.
    <T>:4 samples.

[ Section 1:  Check Input Pheno Done ]

[ Section 2:  Run DMR Algorithm Start ]

Loading required package: IlluminaHumanMethylation450kanno.ilmn12.hg19
<< Find DMR with Bumphunter Method >>
3 cores will be used to do parallel Bumphunter computing.
According to your data set, champ.DMR() detected 8142 clusters contains MORE THAN 7 probes within300 maxGap. These clusters will be used to find DMR.

[bumphunterEngine] Parallelizing using 3 workers/cores (backend: doParallelSNOW, version: 1.0.15).
[bumphunterEngine] Computing coefficients.
[bumphunterEngine] Smoothing coefficients.
[bumphunterEngine] Performing 250 bootstraps.
[bumphunterEngine] Computing marginal bootstrap p-values.
[bumphunterEngine] Smoothing bootstrap coefficients.
Error in { : task 1 failed - "cannot allocate vector of size 56.5 Mb"
In addition: Warning messages:
1: In for (v in val) { :
  closing unused connection 5 (<-LAPTOP-DJ95261D:11153)
2: In for (v in val) { :
  closing unused connection 4 (<-LAPTOP-DJ95261D:11153)
3: In for (v in val) { :
  closing unused connection 3 (<-LAPTOP-DJ95261D:11153)

Any suggestions for how I can fix this?

Best,

R.

[YuanTian1991]

Hi Ron:

Sorry I just saw this. The problem is the memory is not enough. Could you run it on the server?

Best Tian

[ronfinn]

Hi Tian,

Thanks for getting back to me.

I would but I am getting the same error on the server that I got on the local

Running champ.runCombat()...
[===========================]
[<< CHAMP.RUNCOMBAT START >>]
-----------------------------
<< Preparing files for ComBat >>
[Combat correction will be proceed with 403116 probes and 8 samples.]

Error in `.rowNamesDF<-`(x, value = value) : invalid 'row.names' length
In addition: Warning message:
In readLines(csvfile) :
  incomplete final line found on '/mnt/254b78b9-76b4-422d-84b1-cc632bff60f7/Software/install/R-3.6.1/lib64/R/library/ChAMPdata/extdata/lung_test_set.csv'

Best,

Ron

[YuanTian1991]

Hi @ronfinn, could you paste your full command for champ.runCombat() here? I suspect the reason is your Slide batchname is numeric instead fo character.

So maybe you can try:

myLoad$pd$Slide <- as.character(myLoad$pd$Slide)
myCombat <- champ.runCombat()

Best Tian